Sunday, June 21, 2015

How to extract only your modified proteins out of Proteome Discoverer 2.0 results

Hey guys!  Have you been working with Proteome Discoverer 2.0 and ran into a specific question?  Maybe I can figure it out.  This week I popped in on a lab that had a couple of great questions.

The first one is:  How do I extract only proteins with my PTM of interest?  I figured other people might be interested in the answer so I made this video.

Keep the questions coming! I can't guarantee a great turn-around time, but I can sure give it a try.  Honestly, I'm still learning this software, just like the rest of you guys but I don't have specific questions to try out and force me to learn new things.

This video will be added to the PD 2.0 videos over there -->


  1. Thanks Ben. Any idea how to extract Aligned sequences around all PTMs in PD 2.0? This would be extremely useful for phospho-motif analysis!

  2. How to extract PTM proteins out of Proteome Discoverer 1.4 result??